except:
sys.stderr.write('Bad path for working directory. Enter new path or quit("Q"):\n')
PATH = raw_input('')
if PATH.startswith('q') or PATH.startswith('Q'):
sys.exit()
TREE_PATH = "./measuring_%s_tree.nw" % (typ)
ALG_PATH = "./alignment_%s_measuring_evol.fasta" % (typ)
TREE_PATH = PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = PATH + re.sub('\./', '', ALG_PATH )
print T
print '\n ----> and an alignment from: \n'+ALG_PATH+'\n\n'
T.link_to_alignment(ALG_PATH)
raw_input(" ====> hit some key to see the Tree with alignment")
T.show()
###
# run free-branch model, and display result
print '\n\n\n ----> We define now our working directory, that will be created:', \
WORKING_PATH
T.workdir = (WORKING_PATH)
print '\n ----> and run the free-branch model with run_model function:\n\n%s\n%s\n%s\n'\
% ('*'*10 + ' doc ' + '*'*10, T.run_model.func_doc, '*'*30)
raw_input(" ====> Hit some key to start free-branch computation with codeml...\n")
T.run_model('fb')
T.show()
###
# run site model, and display result
except:
sys.stderr.write(
'Bad path for working directory. Enter new path or quit("Q"):\n')
PATH = raw_input('')
if PATH.startswith('q') or PATH.startswith('Q'):
sys.exit()
TREE_PATH = "./measuring_%s_tree.nw" % (typ)
ALG_PATH = "./alignment_%s_measuring_evol.fasta" % (typ)
TREE_PATH = PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = PATH + re.sub('\./', '', ALG_PATH)
print T
print '\n ----> and an alignment from: \n' + ALG_PATH + '\n\n'
T.link_to_alignment(ALG_PATH)
raw_input(" ====> hit some key to see the Tree with alignment")
T.show()
###
# run free-branch model, and display result
print '\n\n\n ----> We define now our working directory, that will be created:', \
WORKING_PATH
T.workdir = (WORKING_PATH)
print '\n ----> and run the free-branch model with run_model function:\n\n%s\n%s\n%s\n'\
% ('*'*10 + ' doc ' + '*'*10, T.run_model.func_doc, '*'*30)
raw_input(
" ====> Hit some key to start free-branch computation with codeml...\n"
)
T.run_model('fb')
T.show()
from ete3.evol import EvolTree
import sys, re
typ = 'S'
#while typ != 'L' and typ != 'S':
# typ = raw_input (\
# "choose kind of example [L]ong or [S]hort, hit [L] or [S]:\n")
TREE_PATH = "data/S_example/measuring_%s_tree.nw" % (typ)
ALG_PATH = "data/S_example/alignment_%s_measuring_evol.fasta" % (typ)
WORKING_PATH = "data/S_example/paml/"
MY_PATH = ''
TREE_PATH = MY_PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = MY_PATH + re.sub('\./', '', ALG_PATH )
T = EvolTree (TREE_PATH)
T.link_to_alignment (ALG_PATH)
T.workdir = (WORKING_PATH)
T.link_to_evol_model(T.workdir + '/fb/out','fb')
T.link_to_evol_model(T.workdir + '/M1/out','M1')
T.link_to_evol_model(T.workdir + '/M2/out','M2')
T.show(histfaces=['M2'])
sys.stderr.write('\n\nThe End.\n\n')
